Habitual sleep duration and sleep duration variation are independently associated with body mass index.

BACKGROUND: Sleep plays a vital role in maintaining homeostasis and promoting health. Previous studies show that shorter sleep duration is associated with elevated body mass index (BMI) and other cardiovascular risk factors. The goal of this study was to investigate the effects of habitual sleep duration and nightly sleep duration variation based on daily device-recorded data on BMI and obesity-related biomarkers. METHODS: In all, 748 individuals (50.6% females, 85.4% European-Americans, average age: 49.7 years old) participated in a commercial lifestyle coaching program beginning in July 2015. Daily sleep data were recorded by Fitbit Charge HR wristbands. Clinical laboratory blood tests were measured up to three times over a 12-month period. Linear regression models were used for cross-sectional analyses, and generalized estimating equations for longitudinal analyses. All models were adjusted for age, sex, geographic location, season, genetic ancestry inferred from whole genome sequencing data, and BMI (if applicable). Multiple testing issues were corrected by false discovery rate. RESULTS: We calculated habitual sleep duration and nightly sleep duration variation. In general, females slept 15-min longer on average than males. A negative correlation was found between habitual sleep duration and BMI (ß=-1.12, standard error=0.25, P<0.001). Moreover, we identified a positive correlation between sleep duration variation and BMI (ß=2.97, standard error=0.79, P<0.001) while controlling for sleep duration, indicating that larger sleep duration variation is significantly and independently associated with increased BMI. CONCLUSIONS: We explored the impact of habitual sleep duration and sleep duration variation, and identified that shorter habitual sleep duration and larger duration variation were independently associated with increased BMI.

Potency of progestogens used in hormonal therapy: toward understanding differential actions.

Progestogens are widely used in contraception and in hormone therapy. Biochemical and molecular biological evidence suggests that progestogens differ widely in their affinities and transcriptional effects via different steroid receptors, and hence cannot be considered as a single class of compounds. Consistent with these observations, recent clinical evidence suggests that, despite their similar progestogenic actions, these differences underlie different side-effect profiles for cardiovascular disease and susceptibility to infectious diseases. However, choice of progestogen for maximal benefit and minimal side-effects is hampered by insufficient comparative clinical and molecular studies to understand their relative mechanisms of action, as well as their relative potencies for different assays and clinical effects. This review evaluates the usage, meaning and significance of the terms affinity, potency and efficacy in different models systems, with a view to improved understanding of their physiological and pharmacological significance. This article is part of a Special Issue entitled 'Menopause'.

The timing of nectar secretion in staminal and staminodial glands in Lauraceae.

The flowers of many Lauraceae have two kinds of glandular organ: paired glands at the base of the filaments of the third androecial whorl, and staminodes with a glandular head, corresponding to a fourth, sterile androecial whorl. So far, it is unknown why there are two different kinds of organ with apparently the same function. Observations now show that the staminal and the staminodial glands secrete nectar at different times in the heterodichogamous flowering cycle, and are therefore essential for the pollination of bisexual Lauraceae flowers.

Control of specific growth rate in Saccharomyces cerevisiae.

In this contribution we resolve the long-standing dispute whether or not the Monod constant (K(S)), describing the overall affinity of an organism for its growth-limiting substrate, can be related to the affinity of the transporter for that substrate (K(M)). We show how this can be done via the control of the transporter on the specific growth rate; they are identical if the transport step has full control. The analysis leads to the counter-intuitive result that the affinity of an organism for its substrate is expected to be higher than the affinity of the enzyme that facilitates its transport. Experimentally, we show this indeed to be the case for the yeast Saccharomyces cerevisiae, for which we determined a K(M) value for glucose more than two times higher than the K(S) value in glucose-limited chemostat cultures. Moreover, we calculated that at glucose concentrations of 0.03 and 0.29 mM, the transport step controls the specific growth rate at 78 and 49 %, respectively.

Summation theorems for flux and concentration control coefficients of dynamic systems.

Metabolic control analysis (MCA) was developed to quantify how system variables are affected by parameter variations in a system. In addition, MCA can express the global properties of a system in terms of the individual catalytic steps, using connectivity and summation theorems to link the control coefficients to the elasticity coefficients. MCA was originally developed for steady-state analysis and not all summation theorems have been derived for dynamic systems. A method to determine time-dependent flux and concentration control coefficients for dynamic systems by expressing the time domain as a function of percentage progression through any arbitrary fixed interval of time is reported. Time-dependent flux and concentration control coefficients of dynamic systems, provided that they are evaluated in this novel way, obey the same summation theorems as steady-state flux and concentration control coefficients, respectively.

Conditions for effective allosteric feedforward and feedback in metabolic pathways.

Whether an allosteric feedback or feedforward modifier actually has an effect on the steady-state properties of a metabolic pathway depends not only on the allosteric modifier effect itself, but also on the control properties of the affected allosteric enzyme in the pathway of which it is part. Different modification mechanisms are analysed: mixed inhibition, allosteric inhibition and activation of the reversible Monod-Wyman-Changeux and reversible Hill models. In conclusion, it is shown that, whereas a modifier effect on substrate and product binding (specific effects) can be an effective negative feedback mechanism, it is much less effective as a positive feedforward mechanism. The prediction is that catalytic effects that change the apparent limiting velocity would be more effective in feedforward activation.

Comparing the regulatory behaviour of two cooperative, reversible enzyme mechanisms.

It is shown that both the reversible Hill equation and a generalised, reversible Monod-Wyman-Changeux equation can give analogous regulatory behaviour when embedded in a model metabolic pathway.

Experimental evidence for allosteric modifier saturation as predicted by the bi-substrate Hill equation.

The cooperative enzyme reaction rates predicted by the bi-substrate Hill equation and the bi-substrate Monod-Wyman-Changeux (MWC) equation when allosterically inhibited are compared in silico. Theoretically, the Hill equation predicts that when the maximum inhibitory effect at a certain substrate condition has been reached, an increase in allosteric inhibitor concentration will have no effect on reaction rate, that is the Hill equation shows allosteric inhibitor saturation. This saturating inhibitory effect is not present in the MWC equation. Experimental in vitro data for pyruvate kinase, a bi-substrate cooperative enzyme that is allosterically inhibited, are presented. This enzyme also shows inhibitor saturation, and therefore serves as experimental evidence that the bi-substrate Hill equation predicts more realistic allosteric inhibitor behaviour than the bi-substrate MWC equation.

Evaluation of a simplified generic bi-substrate rate equation for computational systems biology.

The evaluation of a generic simplified bi-substrate enzyme kinetic equation, whose derivation is based on the assumption of equilibrium binding of substrates and products in random order, is described. This equation is much simpler than the mechanistic (ordered and ping-pong) models, in that it contains fewer parameters (that is, no K(i) values for the substrates and products). The generic equation fits data from both the ordered and the ping-pong models well over a wide range of substrate and product concentrations. In the cases where the fit is not perfect, an improved fit can be obtained by considering the rate equation for only a single set of product concentrations. Due to its relative simplicity in comparison to the mechanistic models, this equation will be useful for modelling bi-substrate reactions in computational systems biology.

Software tools that facilitate kinetic modelling with large data sets: an example using growth modelling in sugarcane.

A solution to manage cumbersome data sets associated with large modelling projects is described. A kinetic model of sucrose accumulation in sugarcane is used to predict changes in sucrose metabolism with sugarcane internode maturity. This results in large amounts of output data to be analysed. Growth is simulated by reassigning maximal activity values, specific to each internode of the sugarcane plant, to parameter attributes of a model object. From a programming perspective, only one model definition file is required for the simulation software used; however, the amount of input data increases with each extra interrnode that is modelled, and likewise the amount of output data that is generated also increases. To store, manipulate and analyse these data, the modelling was performed from within a spreadsheet. This was made possible by the scripting language Python and the modelling software PySCeS through an embedded Python interpreter available in the Gnumeric spreadsheet program.

Is there an optimal ribosome concentration for maximal protein production?

A core model is presented for protein production in Escherichia coli to address the question whether there is an optimal ribosomal concentration for non-ribosome protein production. Analysing the steady-state solution of the model over a range of mRNA concentrations, indicates that such an optimum ribosomal content exists, and that the optimum shifts to higher ribosomal contents at higher specific growth rates.

Experimental supply-demand analysis of anaerobic yeast energy metabolism.

Experimental supply-demand analysis of yeast fermentative energy metabolism shows that control of the glycolytic flux is shared between supply and demand. In glucose limited chemostat cultures the supply block was modulated in a dilution rate change and demand block via a benzoic acid titration. Under these conditions the supply block had a flux control of 0.90 and the demand block a flux control of 0.10.

ThermoKinetic modelling. Membrane potential as a dependent variable in ion transport processes.

We show how to incorporate the membrane potential and its effects on the kinetics of ion transport processes into kinetic models.

Modelling cellular processes with Python and Scipy.

This paper shows how Python and Scipy can be used to simulate the time-dependent and steady-state behaviour of reaction networks, and introduces Pysces, a Python modelling toolkit.

How to distinguish between the vacuum cleaner and flippase mechanisms of the lmrA multi-drug transporter in Lactococcus lactis.

A numerical model of the LmrA multi-drug transport system of Lactococcus lactis is used to explore the possibility of distinguishing experimentally between two putative transport mechanisms, i.e., the vacuum-cleaner and the flippase mechanisms. This comparative model also serves as an example of numerical simulation with the scripting language Python and its scientific add-on Scipy.

Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data.

Sucrose accumulation in developing sugar cane (Saccharum officinarum) is accompanied by a continuous synthesis and cleavage of sucrose in the storage tissues. Despite numerous studies, the factors affecting sucrose accumulation are still poorly understood, and no consistent pattern has emerged which pinpoints certain enzyme activities as important controlling steps. Here, we develop an approach based on pathway analysis and kinetic modelling to assess the biochemical control of sucrose accumulation and futile cycling in sugar cane. By using the concept of elementary flux modes, all possible routes of futile cycling of sucrose were enumerated in the metabolic system. The available kinetic data for the pathway enzymes were then collected and assembled in a kinetic model of sucrose accumulation in sugar cane culm tissue. Although no data were fitted, the model agreed well with independent experimental results: in no case was the difference between calculated and measured fluxes and concentrations greater than 2-fold. The model thus validated was then used to assess different enhancement strategies for increasing sucrose accumulation. First, the control coefficient of each enzyme in the system on futile cycling of sucrose was calculated. Secondly, the activities of those enzymes with the numerically largest control coefficients were varied over a 5-fold range to determine the effect on the degree of futile cycling, the conversion efficiency from hexoses into sucrose, and the net sucrose accumulation rate. In view of the modelling results, overexpression of the fructose or glucose transporter or the vacuolar sucrose import protein, as well as reduction of cytosolic neutral invertase levels, appear to be the most promising targets for genetic manipulation. This offers a more directed improvement strategy than cumbersome gene-by-gene manipulation. The kinetic model can be viewed and interrogated on the World Wide Web at http://jjj.biochem.sun.ac.za.

Mercuric chloride enhances immunoglobulin E-dependent mediator release from human basophils.

Mercuric chloride (HgCl2) is an industrial agent known to cause autoimmune disorders and induce IgE synthesis, which plays a crucial role in the manifestation of allergic diseases. In rodents, the immunomodulatory effects of HgCl2 have been shown to involve the enhancement of mast cell-derived IL-4 secretion, which facilitates both Th2-lymphocyte development and IgE production. In humans, rapid allergen-dependent release of IL-4 and the related cytokine IL-13 from histamine-containing cells occurs primarily in basophils, along with other proinflammatory mediators such as histamine and LTC4. In this study, we therefore investigated the effects of HgCl2 on the release of the above basophil mediators, either due to the compound alone or in conjunction with IgE-dependent stimulation. HgCl2 (10(-9) to 10(-6) M) did not induce mediator secretion alone but significantly enhanced the release of histamine, LTC4, IL-4, and IL-13 caused by anti-IgE. Higher concentrations of HgCl2 (10(-5) to 10(-3) M) strikingly reduced cell viability; however, toxicity varied depending on cell density and incubation time. Removal of HgCl2 following a short incubation with basophils did not reverse the potentiating effects on basophil mediator secretion to anti-IgE and the concentration of free mercury in the supernatants significantly diminished by up to 20% after incubation with the cells, indicating irreversible Hg binding to cells. By upregulating IgE-dependent human basophil mediator release, our results clearly indicate that HgCl2 potentially exacerbates allergic disorders and promotes a Th2-cytokine profile.

Time of drug elimination in chronic drug abusers. Case study of 52 patients in a "low-step" detoxification ward.

The elimination time of illicit drugs and their metabolites is of both clinical and forensic interest. In order to determine the elimination time for various drugs and their metabolites we recruited 52 volunteers in a protected, low-step detoxification program. Blood samples were taken from each volunteer for the first 7 days, daily, urine sample for the first 3 weeks, daily. Urine was analyzed using a fluorescence-polarization immunoassay (FPIA) and gas chromatography/mass spectrometry (GC/MS), serum using GC/MS. The elimination times of the drugs and/or their metabolites in urine and serum as well as the tolerance intervals/confidence intervals were determined. Due to the sometimes extremely high initial concentrations and low cut-off values, a few of the volunteers had markedly longer elimination times than those described in the literature. The cut-off values were as follows: barbiturates II (200ng/ml), cannabinoids (20ng/ml), cocaine metabolites (300ng/ml), opiates (200ng/ml). GC/MS detected the following maximum elimination times: total morphine in urine up to 270.3h, total morphine and free morphine in serum up to 121.3h, monoacetylmorphine in urine up to 34.5h, 11-nor-9-carboxy-delta-9-tetrahydrocannabinol (THC-COOH) in urine up to 433.5h, THC-COOH in serum up to 74.3h, total codeine in urine up to 123h, free codeine in urine up to 97.5h, total codeine in serum up to 29h, free codeine in serum up to 6.3h, total dihydrocodeine (DHC) in urine up to 314.8h, free DHC in urine up to 273.3h, total and free DHC in serum up to 50.1h. Cocaine and its metabolites were largely undetectable in the present study.

Understanding glucose transport by the bacterial phosphoenolpyruvate:glycose phosphotransferase system on the basis of kinetic measurements in vitro.

The kinetic parameters in vitro of the components of the phosphoenolpyruvate:glycose phosphotransferase system (PTS) in enteric bacteria were collected. To address the issue of whether the behavior in vivo of the PTS can be understood in terms of these enzyme kinetics, a detailed kinetic model was constructed. Each overall phosphotransfer reaction was separated into two elementary reactions, the first entailing association of the phosphoryl donor and acceptor into a complex and the second entailing dissociation of the complex into dephosphorylated donor and phosphorylated acceptor. Literature data on the K(m) values and association constants of PTS proteins for their substrates, as well as equilibrium and rate constants for the overall phosphotransfer reactions, were related to the rate constants of the elementary steps in a set of equations; the rate constants could be calculated by solving these equations simultaneously. No kinetic parameters were fitted. As calculated by the model, the kinetic parameter values in vitro could describe experimental results in vivo when varying each of the PTS protein concentrations individually while keeping the other protein concentrations constant. Using the same kinetic constants, but adjusting the protein concentrations in the model to those present in cell-free extracts, the model could reproduce experiments in vitro analyzing the dependence of the flux on the total PTS protein concentration. For modeling conditions in vivo it was crucial that the PTS protein concentrations be implemented at their high in vivo values. The model suggests a new interpretation of results hitherto not understood; in vivo, the major fraction of the PTS proteins may exist as complexes with other PTS proteins or boundary metabolites, whereas in vitro, the fraction of complexed proteins is much smaller.

[A long-term organic brain syndrome and brain stem symptoms in an undiagnosed dialysis-associated encephalopathy]. / Langjähriges Psychosyndrom und Hirnstammsymptomatik bei unerkannter Dialyse-assoziierter Enzephalopathie.

HISTORY AND CLINICAL FINDINGS: A 73-year-old woman in renal failure for the past 22 years had been on haemodialysis for 16 years. Because of hyperphosphataemia and peptic ulcers she had been on aluminium-containing antacids with a total intake over time of about 8 kg "pure" aluminium. Over the past 11 years she had biphasic symptoms of death anxieties and depression. She also had amnesic aphasia and some extrapyramidal symptoms as well as generalized convulsive seizures and recurrent falls. INVESTIGATIONS: Cranial computed tomography merely revealed signs of a microangiopathy and an age-related decrease in brain volume. The EEG showed intermittent changes while the CSF and ECG were unremarkable. There was no benzodiazepine or ethanol in the blood. TREATMENT AND COURSE: After excluding stroke with secondary epilepsy, uraemic encephalopathy was assumed to be the cause of the severe organic psychiatric syndrome. In the last few days before her death the patient had disturbance of consciousness and of breathing. She died during grotesque tossing movements, thought to be due to a brain stem stroke. Autopsy revealed high-grade myocardial hypertrophy caused by the hypertension, contracted kidney of vascular cause, hyperplasia of the parathyroid and calcification of the renal parenchyma as a sign of secondary parathyroidism. The CNS showed severe dialysis-associated encephalopathy with characteristic argyrophilic, aluminium-induced lysosomal intracytoplasmic inclusions in the choroid plexus epithelium, cortical glia and numerous neuron populations. Laser microprobe mass analysis (LAMMA) confirmed manifold increase in subcellular aluminium content, especially in the neuronal cytoplasm, also demonstrated by atom absorption spectrometry. Additional distinct deposition of beta A4-amyloid, typical of Alzheimer's disease, was probably age-related rather than associated with the dialysis and the aluminium uptake. CONCLUSION: Dialysis-associated encephalopathy must be taken into account as a possible cause of aetiologically uncertain neuropsychiatric symptoms in patients on chronic haemodialysis.